[English] 日本語
Yorodumi
- PDB-2wl9: Crystal structure of catechol 2,3-dioxygenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wl9
TitleCrystal structure of catechol 2,3-dioxygenase
ComponentsCATECHOL 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / AROMATIC HYDROCARBONS CATABOLISM / IRON
Function / homology
Function and homology information


: / dioxygenase activity / xenobiotic catabolic process / ferrous iron binding
Similarity search - Function
2,3-dihydroxybiphenyl 1,2-dioxygenase / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase ...2,3-dihydroxybiphenyl 1,2-dioxygenase / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / 3-METHYLCATECHOL / Catechol 2,3-dioxygenase
Similarity search - Component
Biological speciesRHODOCOCCUS SP. DK17 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, H.J. / Kim, K.J. / Kang, B.S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Substrate-Binding Mechanism of a Type I Extradiol Dioxygenase.
Authors: Cho, H.J. / Kim, K. / Sohn, S.Y. / Cho, H.Y. / Kim, K.J. / Kim, M.H. / Kim, D. / Kim, E. / Kang, B.S.
History
DepositionJun 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,04514
Polymers136,2734
Non-polymers77210
Water5,441302
1
C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,85724
Polymers272,5458
Non-polymers1,31216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area23010 Å2
ΔGint-204.3 kcal/mol
Surface area79680 Å2
MethodPISA
2
A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,32332
Polymers272,5458
Non-polymers1,77724
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area24400 Å2
ΔGint-236.4 kcal/mol
Surface area78990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.562, 102.562, 142.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
CATECHOL 2,3-DIOXYGENASE


Mass: 34068.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS SP. DK17 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6REQ5

-
Non-polymers , 5 types, 312 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MBD / 3-METHYLCATECHOL / 3-METHYL-BENZENE-1,2-DIOL


Mass: 124.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 30% PEG 400. 0.1M HEPES PH7.5, 0.2M MAGNESIUM CHLORIDE

-
Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1
DetectorDate: Aug 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.508
11K, H, -L20.492
ReflectionResolution: 1.9→40 Å / Num. obs: 114402 / % possible obs: 99.2 % / Observed criterion σ(I): 1.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.6 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WL3

2wl3


Resolution: 1.9→142.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.922 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN B AND D RESIDUES 178-183 ARE DISORDERD
RfactorNum. reflection% reflectionSelection details
Rfree0.17602 5735 5 %RANDOM
Rwork0.15055 ---
obs0.15184 108666 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.827 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å20 Å2
2--4.3 Å20 Å2
3----8.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→142.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9348 0 41 302 9691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0219734
X-RAY DIFFRACTIONr_bond_other_d0.0070.0219734
X-RAY DIFFRACTIONr_angle_refined_deg1.071.94513241
X-RAY DIFFRACTIONr_angle_other_deg1.071.94513241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63551212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47323.738511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.419151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9691572
X-RAY DIFFRACTIONr_chiral_restr0.0710.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217754
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.55906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71729447
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07633828
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6634.53778
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 422 -
Rwork0.207 7821 -
obs--96.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37340.09540.01930.290.01760.50960.00890.0124-0.02670.00340.0153-0.04240.03490.0386-0.02410.0110.01050.00090.0158-0.01250.0334-29.498631.244233.5636
20.30340.0269-0.06470.48710.03290.41090.0105-0.0421-0.0250.03030.0091-0.06220.0210.0798-0.01960.01080.0024-0.01650.0551-0.00560.0271-21.72751.450272.0688
30.46710.0697-0.03170.1208-0.11520.3592-0.0096-0.01670.04320.01780.0222-0.024-0.0423-0.006-0.01260.0250.00480.00220.0155-0.02520.0462-4.909229.09090.5571
40.4458-0.0980.05650.40080.03120.57670.02480.02660.0575-0.02670.0126-0.0144-0.00820.0286-0.03740.026-0.00910.0170.01040.00210.028315.835524.9587-37.9407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 174
2X-RAY DIFFRACTION1A175 - 245
3X-RAY DIFFRACTION1A246 - 297
4X-RAY DIFFRACTION2B2 - 174
5X-RAY DIFFRACTION2B175 - 245
6X-RAY DIFFRACTION2B246 - 297
7X-RAY DIFFRACTION3C2 - 174
8X-RAY DIFFRACTION3C175 - 245
9X-RAY DIFFRACTION3C246 - 297
10X-RAY DIFFRACTION4D2 - 174
11X-RAY DIFFRACTION4D175 - 245
12X-RAY DIFFRACTION4D246 - 297

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more